Multiple sequence alignment - TraesCS7D01G283400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G283400 chr7D 100.000 6354 0 0 1507 7860 293210756 293217109 0.000000e+00 11734.0
1 TraesCS7D01G283400 chr7D 100.000 1164 0 0 1 1164 293209250 293210413 0.000000e+00 2150.0
2 TraesCS7D01G283400 chr7D 97.203 143 3 1 3369 3510 293212472 293212614 2.830000e-59 241.0
3 TraesCS7D01G283400 chr7D 97.203 143 3 1 3223 3365 293212618 293212759 2.830000e-59 241.0
4 TraesCS7D01G283400 chr7D 86.726 226 17 5 7420 7632 293216552 293216777 1.020000e-58 239.0
5 TraesCS7D01G283400 chr7D 86.726 226 17 5 7303 7528 293216669 293216881 1.020000e-58 239.0
6 TraesCS7D01G283400 chr7D 83.784 222 26 4 7647 7859 337237128 337237348 1.340000e-47 202.0
7 TraesCS7D01G283400 chr7D 83.710 221 26 4 7648 7859 344369644 344369863 4.810000e-47 200.0
8 TraesCS7D01G283400 chr7D 83.408 223 27 4 7647 7860 326841895 326842116 1.730000e-46 198.0
9 TraesCS7D01G283400 chr7D 95.098 102 5 0 7531 7632 293216559 293216660 2.270000e-35 161.0
10 TraesCS7D01G283400 chr7D 95.098 102 5 0 7310 7411 293216780 293216881 2.270000e-35 161.0
11 TraesCS7D01G283400 chr7B 96.485 3898 87 23 3991 7860 358877586 358873711 0.000000e+00 6394.0
12 TraesCS7D01G283400 chr7B 96.838 2530 38 12 1507 4014 358880102 358877593 0.000000e+00 4191.0
13 TraesCS7D01G283400 chr7B 93.579 1168 61 10 1 1164 358881319 358880162 0.000000e+00 1729.0
14 TraesCS7D01G283400 chr7B 84.615 247 37 1 6 251 162986598 162986844 2.190000e-60 244.0
15 TraesCS7D01G283400 chr7B 95.070 142 6 1 3224 3365 358878238 358878098 1.030000e-53 222.0
16 TraesCS7D01G283400 chr7B 96.296 135 4 1 3369 3502 358878368 358878234 3.690000e-53 220.0
17 TraesCS7D01G283400 chr7B 85.116 215 12 6 7314 7528 358874136 358873942 1.340000e-47 202.0
18 TraesCS7D01G283400 chr7B 83.636 220 14 8 7423 7632 358874253 358874046 3.740000e-43 187.0
19 TraesCS7D01G283400 chr7B 93.103 116 7 1 7310 7425 358874043 358873929 1.360000e-37 169.0
20 TraesCS7D01G283400 chr7A 97.456 3577 60 13 3864 7422 339519533 339523096 0.000000e+00 6072.0
21 TraesCS7D01G283400 chr7A 97.670 2103 32 6 1507 3592 339515238 339517340 0.000000e+00 3596.0
22 TraesCS7D01G283400 chr7A 94.024 753 34 7 1 752 339507381 339508123 0.000000e+00 1131.0
23 TraesCS7D01G283400 chr7A 93.515 478 25 4 7385 7860 339523098 339523571 0.000000e+00 706.0
24 TraesCS7D01G283400 chr7A 92.736 413 10 2 752 1164 339514792 339515184 5.290000e-161 579.0
25 TraesCS7D01G283400 chr7A 98.940 283 3 0 3589 3871 339518158 339518440 2.530000e-139 507.0
26 TraesCS7D01G283400 chr7A 97.902 143 2 1 3369 3510 339516969 339517111 6.090000e-61 246.0
27 TraesCS7D01G283400 chr7A 96.503 143 5 0 3223 3365 339517115 339517257 3.670000e-58 237.0
28 TraesCS7D01G283400 chr7A 85.463 227 19 4 7303 7528 339523130 339523343 2.850000e-54 224.0
29 TraesCS7D01G283400 chr7A 87.143 210 8 2 752 961 339508427 339508617 3.690000e-53 220.0
30 TraesCS7D01G283400 chr7A 87.234 141 8 3 7502 7632 339523098 339523238 1.370000e-32 152.0
31 TraesCS7D01G283400 chr7A 89.565 115 10 2 7312 7425 339523243 339523356 2.290000e-30 145.0
32 TraesCS7D01G283400 chr7A 90.566 106 10 0 7424 7529 339522982 339523087 2.960000e-29 141.0
33 TraesCS7D01G283400 chr2A 84.179 335 39 12 318 642 703658621 703658291 5.920000e-81 313.0
34 TraesCS7D01G283400 chr5A 83.758 314 39 11 318 621 529910085 529909774 3.590000e-73 287.0
35 TraesCS7D01G283400 chr5B 85.827 254 32 4 1 252 573183701 573183450 4.680000e-67 267.0
36 TraesCS7D01G283400 chr5B 82.353 255 39 6 1 252 48144473 48144724 4.780000e-52 217.0
37 TraesCS7D01G283400 chr3D 83.137 255 36 6 1 252 18304404 18304154 7.940000e-55 226.0
38 TraesCS7D01G283400 chr3D 81.961 255 42 4 1 252 206971751 206972004 6.180000e-51 213.0
39 TraesCS7D01G283400 chr4B 81.890 254 43 3 1 252 131717718 131717466 2.220000e-50 211.0
40 TraesCS7D01G283400 chr3B 81.890 254 41 5 2 252 717273311 717273562 7.990000e-50 209.0
41 TraesCS7D01G283400 chr6D 83.784 222 26 4 7647 7859 196961025 196960805 1.340000e-47 202.0
42 TraesCS7D01G283400 chr6D 95.918 49 2 0 310 358 438912718 438912766 6.540000e-11 80.5
43 TraesCS7D01G283400 chr6A 83.784 222 26 4 7647 7859 237808106 237807886 1.340000e-47 202.0
44 TraesCS7D01G283400 chr1B 83.784 222 26 4 7647 7859 198669210 198669430 1.340000e-47 202.0
45 TraesCS7D01G283400 chr2D 83.408 223 27 4 7647 7860 267603701 267603480 1.730000e-46 198.0
46 TraesCS7D01G283400 chr1D 83.417 199 22 11 373 562 282138825 282138629 2.920000e-39 174.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G283400 chr7D 293209250 293217109 7859 False 6942.000000 11734 100.000000 1 7860 2 chr7D.!!$F4 7859
1 TraesCS7D01G283400 chr7D 293212472 293216881 4409 False 213.666667 241 93.009000 3223 7632 6 chr7D.!!$F5 4409
2 TraesCS7D01G283400 chr7B 358873711 358881319 7608 True 1664.250000 6394 92.515375 1 7860 8 chr7B.!!$R1 7859
3 TraesCS7D01G283400 chr7A 339514792 339523571 8779 False 1145.909091 6072 93.413636 752 7860 11 chr7A.!!$F2 7108
4 TraesCS7D01G283400 chr7A 339507381 339508617 1236 False 675.500000 1131 90.583500 1 961 2 chr7A.!!$F1 960

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
976 1285 0.034574 CCATCAACCCCCAATCGACA 60.035 55.0 0.00 0.0 0.0 4.35 F
1813 2122 0.603707 CCAGACGTTCCATGTGCTGT 60.604 55.0 0.00 0.0 0.0 4.40 F
2452 2763 0.616679 TGGGCGCTAAGAGGTAAGGT 60.617 55.0 7.64 0.0 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2333 1.402968 CAGAATCAAACATGAGCCGGG 59.597 52.381 2.18 0.00 0.0 5.73 R
2685 3011 4.115516 CGCATCATAGTATATGGTCCAGC 58.884 47.826 0.00 0.00 0.0 4.85 R
7666 10017 3.375782 AAAGTCCAAACAAGAGCATGC 57.624 42.857 10.51 10.51 0.0 4.06 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 7.454260 AAAATCTCCGTAAAATTTCAGCTCT 57.546 32.000 0.00 0.00 0.00 4.09
161 162 6.399743 TGGTAGTTATGCTGAAAACATCGTA 58.600 36.000 0.00 0.00 0.00 3.43
224 225 8.825745 GTCCAAAATAAGAGCAAAATTGTTTGA 58.174 29.630 3.44 0.00 45.99 2.69
256 257 1.844357 CGTTTAGGACGTATCACTGCG 59.156 52.381 0.00 0.00 46.49 5.18
257 258 2.190981 GTTTAGGACGTATCACTGCGG 58.809 52.381 0.00 0.00 34.49 5.69
258 259 1.466856 TTAGGACGTATCACTGCGGT 58.533 50.000 0.00 0.00 34.49 5.68
286 287 9.423061 GCAGTTCCAACAAAGTATTTTCATTAT 57.577 29.630 0.00 0.00 35.03 1.28
471 472 4.028131 AGAATCATACGAACACCTGGGTA 58.972 43.478 0.00 0.00 0.00 3.69
505 506 2.184323 TCGCAGCAGAGAACGAGAT 58.816 52.632 0.00 0.00 0.00 2.75
537 538 4.147449 CTCTGGCGCCGTCATGGA 62.147 66.667 23.90 11.38 42.00 3.41
556 557 2.377628 AAAAGAGAGACCGGCGCACA 62.378 55.000 10.83 0.00 0.00 4.57
578 580 4.436998 GCCACTGCGTAGGCGACT 62.437 66.667 5.26 0.00 44.10 4.18
623 625 1.821061 CGCCTTGGATATCGCCTCCT 61.821 60.000 0.00 0.00 33.69 3.69
664 666 3.073209 TGCCTGACTTGTAAACATACCCA 59.927 43.478 0.00 0.00 0.00 4.51
774 1080 1.400494 ACATATTTTCTCAACCGCGCC 59.600 47.619 0.00 0.00 0.00 6.53
936 1245 0.458370 CACATCACGACGGCATCAGA 60.458 55.000 0.00 0.00 0.00 3.27
964 1273 1.635663 CGTGAACGAGCCCCATCAAC 61.636 60.000 0.00 0.00 43.02 3.18
969 1278 3.346734 GAGCCCCATCAACCCCCA 61.347 66.667 0.00 0.00 0.00 4.96
976 1285 0.034574 CCATCAACCCCCAATCGACA 60.035 55.000 0.00 0.00 0.00 4.35
1071 1380 2.520741 CCAAACACGGCAACCCCT 60.521 61.111 0.00 0.00 0.00 4.79
1715 2024 3.936566 TTCCTCCCGGTGGGTCCT 61.937 66.667 0.00 0.00 44.74 3.85
1813 2122 0.603707 CCAGACGTTCCATGTGCTGT 60.604 55.000 0.00 0.00 0.00 4.40
1859 2170 2.864343 ACTGGATATGTCTTTAACGCGC 59.136 45.455 5.73 0.00 0.00 6.86
1860 2171 1.855978 TGGATATGTCTTTAACGCGCG 59.144 47.619 30.96 30.96 0.00 6.86
2022 2333 0.968393 ACTCCCTTCAGCGAGAGGTC 60.968 60.000 0.00 0.00 41.81 3.85
2248 2559 3.785887 TGGGCTAAGGTACCATGATTTCT 59.214 43.478 15.94 0.00 0.00 2.52
2452 2763 0.616679 TGGGCGCTAAGAGGTAAGGT 60.617 55.000 7.64 0.00 0.00 3.50
2683 3009 2.146342 CTCTTCAGGTGTGCATCGTTT 58.854 47.619 0.00 0.00 0.00 3.60
2685 3011 2.290367 TCTTCAGGTGTGCATCGTTTTG 59.710 45.455 0.00 0.00 0.00 2.44
7635 9982 4.019411 TCAAGCCACCACATTGAATAGAGA 60.019 41.667 0.00 0.00 30.33 3.10
7747 10098 9.016438 TCTGTCATTTTGATCATGAATCTTTGA 57.984 29.630 0.00 0.00 35.24 2.69
7804 10155 6.112927 ACACATGCTAAATGGGTTGAATTT 57.887 33.333 0.00 0.00 30.22 1.82
7809 10160 7.769970 ACATGCTAAATGGGTTGAATTTATTGG 59.230 33.333 0.00 0.00 31.03 3.16
7818 10169 7.983363 TGGGTTGAATTTATTGGGATTTTTCT 58.017 30.769 0.00 0.00 0.00 2.52
7854 10205 8.328758 TGGACACAAGAAAGATATAGAAATGGT 58.671 33.333 0.00 0.00 0.00 3.55
7855 10206 9.832445 GGACACAAGAAAGATATAGAAATGGTA 57.168 33.333 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 7.655328 CAGATAGAGCTGAAATTTTACGGAGAT 59.345 37.037 0.00 0.00 38.14 2.75
135 136 7.045416 ACGATGTTTTCAGCATAACTACCATA 58.955 34.615 0.00 0.00 35.78 2.74
161 162 8.398878 TGATTTAAATGAAACTAACCCGACTT 57.601 30.769 5.17 0.00 0.00 3.01
206 207 7.397970 CGCTTTTTCAAACAATTTTGCTCTTA 58.602 30.769 0.00 0.00 41.78 2.10
224 225 3.059665 CGTCCTAAACGTAACCGCTTTTT 60.060 43.478 0.00 0.00 46.42 1.94
286 287 4.424711 GAGGGTGATTGCCGGGCA 62.425 66.667 19.77 19.77 36.47 5.36
458 459 0.250124 TGCTTGTACCCAGGTGTTCG 60.250 55.000 0.00 0.00 0.00 3.95
471 472 1.668294 CGAGTCTCCTGGTGCTTGT 59.332 57.895 0.00 0.00 0.00 3.16
505 506 1.606601 AGAGGTGCTGTCGCTGGTA 60.607 57.895 0.00 0.00 36.97 3.25
533 534 0.108138 CGCCGGTCTCTCTTTTCCAT 60.108 55.000 1.90 0.00 0.00 3.41
537 538 1.668151 GTGCGCCGGTCTCTCTTTT 60.668 57.895 4.18 0.00 0.00 2.27
623 625 3.303526 GGCAAAGCGTTTTTCTTCTCGTA 60.304 43.478 0.00 0.00 0.00 3.43
774 1080 2.498481 TGGGTTTGACCGATACTGTAGG 59.502 50.000 0.00 0.00 39.83 3.18
936 1245 2.981909 TCGTTCACGGCGAGGAGT 60.982 61.111 16.62 0.00 40.29 3.85
1715 2024 2.968574 GCCTAGAGATGGATGGAGAACA 59.031 50.000 0.00 0.00 0.00 3.18
1813 2122 2.265367 TCCACCAGATTTCCTACAGCA 58.735 47.619 0.00 0.00 0.00 4.41
1859 2170 2.180276 CCTAATCCCAGATCCTACCCG 58.820 57.143 0.00 0.00 0.00 5.28
1860 2171 2.157989 ACCCTAATCCCAGATCCTACCC 60.158 54.545 0.00 0.00 0.00 3.69
2022 2333 1.402968 CAGAATCAAACATGAGCCGGG 59.597 52.381 2.18 0.00 0.00 5.73
2248 2559 6.312399 ACTTGACATGAAATTAAGCGACAA 57.688 33.333 0.00 0.00 0.00 3.18
2603 2920 4.153117 CAGTCCAGAAAACAGAGCATACAC 59.847 45.833 0.00 0.00 0.00 2.90
2683 3009 5.491070 GCATCATAGTATATGGTCCAGCAA 58.509 41.667 0.00 0.00 0.00 3.91
2685 3011 4.115516 CGCATCATAGTATATGGTCCAGC 58.884 47.826 0.00 0.00 0.00 4.85
3040 3371 7.330208 CACAAATCTGAAGATGGGAAAACATTC 59.670 37.037 0.00 0.00 34.49 2.67
7666 10017 3.375782 AAAGTCCAAACAAGAGCATGC 57.624 42.857 10.51 10.51 0.00 4.06
7711 10062 8.868522 TGATCAAAATGACAGATTCTTTAGGT 57.131 30.769 0.00 0.00 0.00 3.08
7722 10073 9.634163 TTCAAAGATTCATGATCAAAATGACAG 57.366 29.630 0.00 0.00 37.22 3.51
7804 10155 7.877097 CCAATGACACAAAGAAAAATCCCAATA 59.123 33.333 0.00 0.00 0.00 1.90
7809 10160 6.279882 TGTCCAATGACACAAAGAAAAATCC 58.720 36.000 0.00 0.00 46.40 3.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.